Irreproducible Results

In my BBS days (probably in 1992) I stumbled upon an interesting text file. It claimed to contain the instructions to build a nuclear bomb! It was formatted in a sensible manner and written in good English. The content was highly entertaining, though I wasn't sure if smoke detectors' americium is really fissible material.

Alright, the text was from The Journal of Irreproducible Results - I think the text was titled "Let's Build a Nuclear Bomb". At the end of the file, there were teasers of other articles, such as "Let's Build a Solar System" or "Let's Make Contact With an Extra-Terrestrial Civilization" (if I recall correctly). Sounds entertaining but not really reproducible.

Is research supposed to be reproducible? If you read a research paper and take a look at its fancy charts and other visualizations, can you actually reproduce the results? If the paper claims a discovery that enables you to build an atomic bomb out of smoke detectors, can you prove it right or wrong? (Sure, a paper like that would probably not pass peer review phase, but hypothetically...)

Today - 20 years after I found the text about building a nuclear bomb - research often involves huge amounts of data. Often, that data is actually proprietary. The results may be entirely based on secret data that is not available to anyone, and cannot be (easily) generated by anyone else than its owner and generator. Still, the research can be held in great value - actually, that is how different products are certified for use.

As astonished I am about the fact that reproducing results is difficult, I am also about the fact that some have actually acknowledged the problem within the scientific community and developed tools and approaches to alleviate it. Lately, I have been looking at knitr which is an R module for dynamic report generation. Using knitr, there can be a direct link between the document and the original data set(!). Another interesting approach is lightweight markup languages such as Markdown which I evaluated in my bachelor's thesis some years ago. In a way, this is "open source research", where you open up the methods and data to anyone who is interested in them.

As a sidenote: Some years ago, the Finnish-language Master's thesis Kotileikkejä ja lastenkasvatuspuuhia was written by Juhapekka Tolvanen. An important aspect - though in no way related to the topic of this thesis in the field of sociology - was that it was released with the GNU Free Documentation License and the LaTeX source code was (and is) downloadable from the author's homepage, thus making the thesis printable and publishable in different formats. However, plain LaTeX source code is not very readable (though Mr. Tolvanen might disagree) - and most of the formatting of the actual text content could have been done with Markdown.

For smaller projects it is maybe easier to incorporate transparency, distribution of data sets used in the research and demonstrating exactly how the results were produced, but can this approach be more widely adopted by peer-reviewed journals? For that, I don't know the answer, I just know the direction where I would like them to go and where I will go.

My problems with Prometheus

Everyone wants to complain about Ridley Scott's Prometheus. Everyone has their reasons and so do I. I have a blog, so I must write something, right?

Trailer

The problems start with the trailer. What do we know after seeing this?

• Scientists go to find their creator, or ancient humans.
• They find a deserted temple of some kind.
• It turns out that it isn't deserted after all - it is Space Jockeys' base! Space Jockeys are human and they created us for some purpose!
• There are alien eggs (or something) around there.
• Chaos ensues and people (presumably) die one by one.
• Humans' spaceship is destroyed in a collision with some other object (presumably trapping humans on the planet that they found).
• A circular object drops from the sky or is otherwise falling on the ground.

Even before any trailers, the director gave hints that the events in this movie happen in the Alien universe before the time of the first Alien movie, but there are no Xenomorphs in this one. Instead, this movie shall in some way explore what the Space Jockeys are.

It would be disappointing if those observations from the trailer would appear correct, wouldn't it?

Movie

I think the movie was pretty enjoyable with some suspense, though no humor or horror elements. Special effects were relatively entertaining, but they were also quite generic CGI.

Spoiler: All of the above observations from the trailer ended up being totally correct.

I'll list my principal problems with the movie here.

• General lack of motivation or sense of purpose. Things happen but there is no real reason for them to be happening. What triggered them? Ghost in the machine or some real mechanism that is supposed to be contained in the scenario?
• Talk about the lack of aliens. Of course there are aliens here, it was revealed right in the trailer. Maybe there were not exactly the same type of adult Xenomorphs that we saw in the previous movies but aliens anyway.
• Where do the baby aliens get all the biomass? How can they grow to fill a room in a day without eating anything?
• Why do the scientists remove the helmets? It should be in the basic training of field work that you shall not contaminate the place. Also, if the alien planet has the same kind of atmosphere (including pressure) that Earth has, same kind of bacteria can also live there. Why did they not think about this? (Granted, Shaw is pretty cute.)
• Shaw & co. went pretty far before seriously suspecting that there was something sinister in the company's motives behind funding this trip.
• Even though the human entourage is full of scientists, there is no scientific discussion about what is happening. Things are just noted and accepted without questions.
• When the captain notices that the cave forms a circle, he immediately knows that it is a spaceship and announces it. Everyone believes him. Why? In the Alien universe, spaceships do not look like circles. There is no apparent propulsion, crew areas, antigravitation, fuel, sophisticated control surfaces or other mechanisms that a spaceship would probably have.
• Even when this spaceship started to levitate, it should not have been apparent that it was a spaceship. In the Alien universe, spaceships do not levitate - they have motors. 
• When they arrive at this planet, why does the ship accelerate towards the planet? Shouldn't they be decelerating at that point?
• It is difficult to conceive why the crew of Prometheus were so happy to kill themselves.
• Why does David think that he could fly one of those ships? Are they made for children to fly?
• Umm, why was the old guy on the ship?
• Why was this movie released in 3D?!

That's it. A clever science fiction flick that plays with mystery, cool effects and aliens. Extremely predictable, especially after seeing the trailer. Why?

Error messages and invalid error messages

Error messages are necessary evil. If something goes really wrong, the user must know. However, they should always be useful - otherwise they should not be displayed, right? They should also be correct.

I use Foursquare on my Android phone. Every once in a while, in the maze of different Wi-Fi hotspots at University of Michigan Central Campus, the phone switches from mobile data to Wi-Fi and back. And does something, I couldn't care less. Foursquare apparently has a problem with this and it complains.

"Foursquare connection invalid", it says. Well, I can clearly see that at the moment there is no Internet connection at all, so how can Foursquare have a connection in the first place? How can I fix Foursquare's connection if there is no connection? Even if there was, what should I do?

"No Internet connection" is also a bad error message, especially when I am connected to Internet. If Foursquare has trouble connecting to its own servers, it should not give error messages about my phone's connection in general.

I know that switching between mobile data and Wi-Fi hotspots can be challenging connection-wise. However, shouldn't Wi-Fi connections make connectivity better, faster and more convenient? Actually, at the campus, the phone tries to connect Wi-Fi hotspots here and there, thus immediately abandoning the mobile data, even before actually establishing connection. The result may be that there is no network connection for long periods of time. This can be fixed by not using Wi-Fi at all, or "forgetting" all networks that the phone tries to connect. There is no "Disconnect" - they must be forgotten, at least on Samsung Galaxy S II.

Why I would not vote for Ron Paul for President

Ron Paul is one the four most prominent candidates in the race to be nominated as the Republican Party's presidential candidate, to run against Democrats' Barack Obama in 2012. Newspapers and social media websites are full of quotes from GOP debates - making it pretty obvious to me that most of the well-known Republican candidates are idiots.

I am (kind of) sorry for that expression, but I cannot avoid the impression I have got from the remarks they have made. Bachmann, Perry and Santorum are just way out of line and Cain did not seem to be smart enough to understand what's wrong with his message. Newt Ginrich is somehow just a boring, repulsive professional politican (with lots of experience) and Mitt Romney a less repulsive but just as boring politician. If I have counted correctly, that leaves out Ron Paul. Because I know many smart people who share (some part of) libertarian ideals, I thought I should write this blog post to explain why I (even though I am smart!) would not vote for him.

Many of the Republican stereotypes do not apply to Ron Paul; he does not seem to want to have a system that pushes his personal (religious or political) beliefs down everyone's throat. He is undeniably bold and intelligent and is not afraid of being at odds with even fellow Republicans. But of course, he is not a Republican at heart, he is libertarian and happens to be playing with Republicans out of necessity, as in United States you must be with the Democrats or Republicans in order to achieve any political offices.

I sincerely hope that Ron Paul wins the Republican nomination, for many reasons. It would be a shock to Republicans and may force them to rethink many policies, interventionist doctrines and so on. It would also make the future debates with Barack Obama much more interesting. He is very much "electable" but not probable to win. Against Obama, I think Paul would be the wrong choice (but I think Paul will try to get nominated every four years as long as he is alive). I am happy not to be writing about this as a U.S. citizen, so I do not have to make a choice and vote, because I do not like the U.S. political system in general.

The Ron Paul Newsletters - or different publications that were published under Ron Paul's name but him apparently not being aware what was being published - are a difficult matter. I know that Paul has said it was stupid not to have any knowledge of the stuff that the publications contained. They had a lot of text that would be considered racist, bigotry, conspiracy theories and so on. I find it very difficult to understand how a prominent businessman and politician could be so ignorant of what is published under his name, how can he screw up so badly?

As a politician, Ron Paul does not really have a track record of cooperation and going by the general opinion of his partymates or the government's. As a president, who leads the whole country, that is a major problem. Obama is criticized as being "too negotiating" and not taking enough stance on matters,  but I fear that Paul would be far too independent and constantly at odds with Congress and Senate. As a result, it would be difficult for him to push through any new policies, and as everybody knows, he has plenty of them. I am not convinced of his ability in making compromises in matters that he has declared as critically important.

I think many of the libertarian ideals that Paul upholds make a lot of sense. However, I do not think it is the best way to advance them to have a libertarian president who must fight the Senate and the Congress who very much disagree with those ideals. I know that libertarians believe that having no (or very little) taxes, no mandatory or state-provided health insurance etc. would contribute to a better world, more liberty, more jobs and less poverty. I do not believe that. Like communism, libertarianism would not work. Instead, both of them are useful and many of their ideals can be used in real world.

I am also worried about Paul's stance towards abortion. He regards an embryo a "person". This would mean that abortion is for some purposes, among other things, a murder. I dislike the American polarized discourse about abortion, but I do not think that abortion should be classified as murder (intentional killing of a person).

Even though I generally support Paul's ideals about not interfering other countries' matter so much, not waging war and not spending so many trillions of dollars into military (especially with budget deficit), I think his proposals are a too unrealistic again. The operations in Iraq and Afghanistan have left United States with obligations that it cannot just abandon like that.

I also don't like Paul getting money from a Ku Klux Klan leader and being satisfied with the donations. However, this might not be as big an issue as it has been advertised to be.

So, is Ron Paul, or would he be, a good leader? Caring yet strong, understanding of issues both domestic and foreign? Does he have friends, does he make friends? Is his view of the world correct? I think not.

Presidential Candidate Poll: How to Fail in Visualizing the Results

How difficult can it be to produce a simple bar graph out of poll results? For the Finnish media corporation MTV3 it is at least very challenging. As I am currently studying, among other things, information visualization at University of Michigan, I got an irresistible temptation to try to analyze some of the problems one of their visualizations has.

On Wednesday, November 9, MTV3.fi published an article "Niinistö still superior candidate, others far behind" (translation mine), with the most recent poll results. The poll was conducted by telephone by Research Insight Finland. The exact number of interviewed people was not revealed in the article but it was "a bit more than one thousand". (N=1002 as revealed in the other graph attached to the article.) The error marginal was ±3.1 %.

There original graph is below. It has been copied from the article, so if it is fixed later, those revisions will not be visible here.

General

Just a couple of observations about the graph in general. There cannot be links contained in an image, so the text "suurenna kuva" ("magnify the image") is not a link. It just should not be there. The title of the graph is differentiated from the other one(s) just by the addition of "Alue" ("Area") at the end. Why not "alueittain" ("by the area") or if they are using some formal way of dividing the country into divisions (see below), they could reveal it here.

Bars and data

The scale of the graph goes from 0 to 100. What are the units? We can guess they are supposed to be the percentage of respondents choosing a specific option in the poll... What is the point of extending the scale up to 100 %? The most popular choice is still less than 50 % and because of this scale, the differences between the less popular candidates are impossible to see. The labels for the bars have no decimals, so Paavo Arhinmäki's popularity data per province is just "1, 1, 1, 2, 1". What's even more worrying: the bars are based on results after rounding them to the nearest integer, not on the actual values!

It could be said that the bars fail to give any real insight into the results because of this mistakes. But wait! There is an even more severe error below them. In the poll there were ten options but there are only nine labels in this graph. The labels are evenly spread, so they are also misaligned. Especially the least popular candidate's names are difficult to associate with the related bars - does Sari Essayah have popularity of 1 % or 19 %? The mistake: they forgot to put a label for "undecided"!

Also: if the question is "Who would you vote if the elections were held right now?", the answer must be in partitive form - Sauli Niinistöä, Timo Soinia, Paavo Väyrystä (his name is misspelled in the labels, with lower case v!) and so on. "En ketään ylläolevista" ("None of the above") is in the correct form, but there are no names above it (only on the left), so which names does it refer to? As this poll was conducted by telephone, how did the interviewees know which names were above this option and which in other directions?

Legend

In the legend on the right, the explanations for the five bars of different color are given. For the purposes of this graph, the results of the poll were divided geographically along the administrative provinces - lääni in Finnish. Here lies one problem: there are no provinces in Finland any more! In this graphs, the division is (probably) based on the provinces in use between 1997-2009 - except that there were six of them, not four. Three of them have been named, but all of them were misspelled:

• Eteläsuomen Lääni (Province of Southern Finland - should be spelled as Etelä-Suomen lääni)
• Länsisuomen Lääni (Province of Western Finland - should be spelled as Länsi-Suomen lääni)
• Itäsuomen Lääni (Province of Eastern Finland - should be spelled as Itä-Suomen lääni)
• Pohjois-Suomi (Northern Finland - there has never been a province called this, this is probably Provinces of Oulu and Lapland combined)
• (The Province of Åland Islands is completely missing, probably combined with the first one)

Also, "Total" is not Finnish. It should be "Yhteensä".

I am, of course, only listing the mistakes I spotted. I think the colors are alright and after correcting these, it would not be a bad bar plot at all. Maybe photos of the candidates would make it easier to assiate a candidate with the bars.

Accidental informality

Sometimes I like to think that in the 1990's (or at least before the Eternal September, but then I wasn't online yet) Internet and its services were somehow well organized and people knew how to use them. It isn't true, of course, but some things were better. Email was plain text and messages contained a well-formed signature - often set by the system administrator. This was my experience at Helsinki University of Technology in 1997.

Today, emails can be html, there might not be a plain text part at all, they might have background colors, images and even animations. Instead of a well-formed signature, there might be none or maybe a huge company logo. Even in official communications, you might get no hints of the identity of the sender of the email

Let's take an imaginary example of how emails often look like...

From: caw@umich.edu
To: mstuomel@umich.edu
Subject: Meeting tomorrow

Hi! Shall we meet tomorrow at 5:00 PM?

Cathy

Alright... Who is this person anyway? Some female member of the University of Michigan academic community, I would imagine. Her (nick)name is Cathy and her username seems to be caw. I might or might not find more information with Google or University of Michigan's search engine.

What if I need to contact her to tell I am late? Her email does not contain a phone number, or her faculty home page's URL. It does not even contain her real name. It might be Cathryn A. Witgenstein or Katrina Wu from what I know. She does not care or she does not realize that she should care.

This another imaginary example from the 1990's would be better:

From: Catherine A. Winston <caw@umich.edu>
To: Mikko Tuomela <mstuomel@umich.edu>
Subject: Meeting tomorrow

Hi! Shall we meet tomorrow at 5:00 PM?

--
Catherine A. Winston
Associate Professor, University of Michigan School of Information
caw@umich.edu | (734) 123-4567 | http://www.si.umich.edu/people/caw

Ah! Now I have all the relevant information and also a web address where I can find more.

This post was inspired by all the emails I have received through the years. Don't be offended if you think you have inspired me!

Letting the kids decide for themselves

A common argument for teaching Creationism (or Intelligent Design) in public schools is that we should let the kids decide for themselves which seems correct, so we would respect their intelligence and freedom and so on. This seems to be what the Republican Governor of Texas Rick Perry - also a presidential candidate - believes.

There is one problem. Evolution is the prevailing theory explaining the origin of species and it is backed by science. If other scientific theories (and the scientific method in general) should be challenged in the classroom by non-scientific (or scientific but very unpopular) theories, the curriculum would be pretty absurd. This is actually the easy part.

But what about things that are not exactly science but questions of ethics, politics and so on? I would assume that Texans take certain things for granted - for example that you are allowed to defend yourself and your property or that you are allowed to start your own business, or marry whoever you wish. What if these "beliefs" would be required to be challenged in the classroom?

Consider these debates:

• Socialism vs. Free market economy: Even though USA is generally in favor of free markets, why should the children be taught that this is the default or the best system? Why not Communism? Many things are better in Cuba than in United States, and Soviet Union's society had many advantages over the American one.
• Militarism vs. Pacifism: There is a considerable amount of known thinkers in favor of non-violent resistance, pacifism and generally peaceful conflict resolution. I think Jesus, Mahatma Gandhi and John Lennon would be among these. Still, the situation where U.S. military conducting combat operations around the world does not seem to be challenged. Where is the challenge of this prevailing view, that violence can be justified?
• Consumerism vs. Environmentalism: People consume and produce trash and pollution. That's very natural in United States and it is not going to change. Why not? The natural resources are not infinite and climate seems to be shifting - so why is this not taught at schools, challenging the traditional ways of the society?
• Government vs. Anarchy: Americans seem to be proud of their country, their flag, their liberty and independence. But shouldn't other options be discussed in the classroom, too? The philosophy of anarchy, despising governmental control and authority, could be very interesting to kids. Most Texans also know Jesus, who has often been described as an anarchist thinker of some kind. 

If evolution should be challenged, why shouldn't other models about how the world work? You know, we should not feed "the American way" to the kids, we should let them decide for themselves if they want to follow the teachings of Martin Luther King, Mao Zedong, Adolph Hitler, Ron Paul, Robert Heinlein, Jesus, Vladimir Lenin or George Washington, right?

How far would you go letting them decide for themselves?